| mkFluo4DirectFit {CalciOMatic} | R Documentation |
The function mkFluo4DirectFit defines a single signal made of
four fluorescence signals (the background and fluorescence transients
at both wavelengths), for use with within the
mkFunction4DirectFit function
mkFluo4DirectFit(Ca, phi, S_B_340, S_B_380, nb_B,
R_min, R_max, K_eff, K_d, B_T,
T_340, T_380, P, P_B, SQRT = TRUE)
Ca |
the time course of the intracellular calcium concentration |
phi |
the scaling experiment-specific parameter |
S_B_340 |
the background fluorescence at 340 nm |
S_B_380 |
the background fluorescence at 380 nm |
nb_B |
the number of background measurements |
R_min |
the minimum fluorescence ratio between the measurements at 340 and 380 nm. This parameter is obtained from calibration experiments |
R_max |
the maximum fluorescence ratio between the measurements at 340 and 380 nm. This parameter is obtained from calibration experiments |
K_eff |
the effective dissociation constant of the dye in the cell (in muM). This parameter is obtained from calibration experiments |
K_d |
the dissociation constant of the dye in the cell (in muM). This parameter is obtained from calibration experiments |
B_T |
the total concentration of the dye inside the cell (in muM) |
T_340 |
the exposure time at 340 nm |
T_380 |
the exposure time at 380 nm |
P |
the number of pixels of the ROI |
P_B |
the number of pixels of the background region |
SQRT |
a logical value. Set to TRUE to apply the square
root transformation to the fluorescence signals |
a vector containing, in this order: the background fluorescence (in
count) at 340 nm, the fluorescence transient at 340 nm, the background
fluorescence at 380 nm and the fluorescence transient at 380 nm. If the
SQRT argument is set to TRUE, the square root of the
whole signal is returned
Sebastien Joucla sebastien.joucla@parisdescartes.fr
mkFunction4DirectFit,
directFit
## Parameters of the biexponential calcium transient
tOn <- 1
Time <- seq(0,12,length.out=160)
Ca0 <- 0.10
dCa <- 0.25
tau <- 1.5
mu <- 0
dtau <- 10
## Calibration parameters
R_min <- 0.136
R_max <- 2.701
K_eff <- 3.637
K_d <- 0.583
## Experiment-specific parameters
nb_B <- 1
B_T <- 100.0
T_340 <- 0.015
T_380 <- 0.006
P <- 200
P_B <- 200
phi <- 2
S_B_340 <- 30
S_B_380 <- 80
## Create a biexponential calcium decay
Ca_Bi <- caBiExp(t=Time,
tOn=tOn,
Ca0=Ca0,
dCa=dCa,
tau=tau,
fact=1/(1+exp(-mu)),
dtau=dtau)
## Define the whole original fluorescence vector
Fluo_bi <- mkFluo4DirectFit(Ca = Ca_Bi, phi,
S_B_340, S_B_380, nb_B,
R_min, R_max, K_eff, K_d,
B_T, T_340, T_380, P, P_B,
SQRT = TRUE)